Biology subjects

Zmurchok, C.

Publications and source records attributed to Zmurchok, C..

3 recordsLinked to original sources

bioRxiv2021

Biophysical Models of PAR Cluster Transport by Cortical Flow in C. elegans Early Embryogenesis

The clustering of membrane-bound proteins facilitates their transport by cortical actin flow in early Caenorhabditis elegans embryo cell polarity. PAR-3 clustering is critical for this process, yet the bio-physical processes that couple protein clusters to cortical flow remain unknown. We develop a discrete, stochastic agent-based model of protein clustering and test four hypothetical models for how clusters may interact with the flow. Results show that the canonical way to assess transport characteristics from single particle tracking data used thus far in this area, the Peclet number, is insufficient to distinguish these hypotheses and that all models can account for transport characteristics quantified by this measure. However, using this model, we demonstrate that these different cluster-cortex interactions may be distinguished using a different metric, namely, the scalar projection of cluster displacement on to the flow displacement vector. Our results thus provide a testable way to use existing single particle tracking data to test how endogenous protein clusters may interact with the cortical flow to localize during polarity establishment. To facilitate this investigation, we also develop both improved simulation and semi-analytic methodologies to quantify motion summary statistics (e.g., Peclet number and scalar projection) for these stochastic models as a function of biophysical parameters.

biophysics↗

bioRxiv2020

Membrane tension can enhance adaptation to maintain polarity of migrating cells

Migratory cells are known to adapt to environments that contain wide-ranging levels of chemoattractant. While biochemical models of adaptation have been previously proposed, here we discuss a different mechanism based on mechanosensing, where the interaction between biochemical signaling and cell tension facilitates adaptation. We describe and analyze a model of mechanochemical-based adaptation coupling a mechanics-based physical model of cell tension coupled with the wave-pinning reaction-diffusion model for Rac activity. Mathematical analysis of this model, simulations of a simplified 1D cell geometry, and 2D finite element simulations of deforming cells reveal that as a cell protrudes under the influence of high stimulation levels, tension mediated inhibition of GTPase signaling causes the cell to polarize even when initially over-stimulated. Specifically, tension mediated inhibition of GTPase activation, which has been experimentally observed in recent years, facilitates this adaptation by countering the high levels of environmental stimulation. These results demonstrate how tension related mechanosensing may provide an alternative (and potentially complementary) mechanism for cell adaptation. Statement of SignificanceMigratory cells such as human neutrophils encounter environments that contain wide-ranging levels of chemoattractant. In order to move, these cells must maintain an organized front-rear signaling polarity despite this wide variation in environmental stimuli. Past research has demonstrated a number of biochemical based mechanisms by which cells adapt to variable signal levels. Here we demonstrate that the interplay between Rho GTPase signaling and tension mediated feedbacks may provide an alternative mechanochemical mechanism for adaptation to high levels of signaling.

systems biology↗

bioRxiv2019

Modeling cell shape diversity arising from complex Rho GTPase dynamics

It is well known that cells exhibit a variety of morphologically distinct responses to their environments that manifest in their cell shape. Some protrude uniformly to increase substrate contacts, others are broadly contrac-tile, some polarize to facilitate migration, and yet others exhibit mixtures of these responses. Prior imaging studies have identified a discrete collection of shapes that the majority of cells display and have demonstrated links between those shapes and activity levels of the cytoskeletal regulators Rho GTPases. Here we use a novel computational modeling approach to demonstrate that well known Rho GTPase signaling dynamics naturally give rise to this diverse but discrete (rather than continuum) set of morphologies. Specifically, the combination of auto-activation and mutually-antagonistic crosstalk between GTPases along with the conservative membrane (un)binding dynamics readily explain at least 6 of the 7 commonly observed morphologies. We further use this methodology to map the entire parameter space of this model and show that in appropriate regimes, individual parameter sets give rise to a variety of different morphologies. This provides an explanation for how seemingly similar cells of the same fate derived from the same population can exhibit a diverse array of cell shapes in imaging studies. These results thus demonstrate that Rho GTPases form the core of a cytoskeletal regulatory system governing cell shape, further supporting the picture that they act as a central signaling hub determining how cells respond to their environmental context.

biophysics↗